Is imidazo[1,5-a]pyridine aromatic?

User fca09bdbff

19-02-2010 09:30:38


I noticed that the Aromatic Ring Count descriptor considers imidazo[1,5-a]pyridine, c1ncn2ccccc12, not to be fully aromatic (i.e. one aromatic ring and one aliphatic ring).

However, if one 'aromatizes' the structure in MarvinSketch, both rings are shown as aromatic.

Which is correct?

Regards, Tim Ritchie.

ChemAxon d76e6e95eb

19-02-2010 10:16:22

Two aromatic rings are provided both by Marvin and TopologyAnalyser for me.

cxcalc -N ih "c1ncn2ccccc12" aromaticRingCount

Which version of the software do you use? How can we reproduce the problem?

User fca09bdbff

19-02-2010 11:01:46

Interesting. In MarvinSketch 5.2.4 and 5.2.5, if you aromatize the structure first the ring count is 1 aromatic + 1 aliphatic. If you don't aromatize the structure the result is 2 aromatics!

I ran a large number of molecules through cxcalc, and this ring system was classed as 1 aromatic + 1 aliphatic. I'll run some again and check...

Regards, Tim Ritchie.

User fca09bdbff

19-02-2010 11:18:57

Further to my last post,

In cxcalc, c1cn2ccccc2n1 gives the output 1 aromatic + 1 aliphatic ring, whereas C1=CN2C=CC=CC2=N1 gives 2 aromatic rings.

Thus it appears that the 'aromatic' SMILES is perceived differently...

Regards, Tim Ritchie.

ChemAxon 25dcd765a3

19-02-2010 17:37:32


Thank you for the report.

The bug has been fixed in Marvin 5.3 already.